BMRBj - BMREntryMaster

	Total	¹H	¹³C
All	72.2 % (351 of 486)	88.3 % (248 of 281)	50.2 % (103 of 205)
Backbone	80.6 % (145 of 180)	98.6 % (72 of 73)	68.2 % (73 of 107)
Sidechain	70.7 % (241 of 341)	84.6 % (176 of 208)	48.9 % (65 of 133)
Aromatic	53.0 % (44 of 83)	100.0 % (44 of 44)	0.0 % (0 of 39)
Methyl	100.0 % (36 of 36)	100.0 % (18 of 18)	100.0 % (18 of 18)

1. 10E8p

KKKKDKWASL WNWFDITNWL WYIKLFIMIV GKKKKK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	10E8p	natural abundance	protein	0.5 mM
2	HFIP	[U-2H]		25 % v/v
3	HEPES	natural abundance	buffer	2 mM
4	DSS	natural abundance		0.1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	10E8p	natural abundance	protein	0.5 mM
8	HFIP	[U-2H]		25 % v/v
9	HEPES	natural abundance	buffer	2 mM
10	DSS	natural abundance		0.1 mM
11	D2O	[U-2H]	solvent	100 %

Chem. Shift Complete2

Sequence coverage: 86.1 %, Completeness: 54.8 %, Completeness (bb): 54.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	54.8 % (533 of 972)	75.1 % (422 of 562)	27.1 % (111 of 410)
Backbone	54.2 % (195 of 360)	78.1 % (114 of 146)	37.9 % (81 of 214)
Sidechain	55.1 % (376 of 682)	74.3 % (309 of 416)	25.2 % (67 of 266)
Aromatic	50.0 % (83 of 166)	94.3 % (83 of 88)	0.0 % (0 of 78)
Methyl	72.2 % (52 of 72)	94.4 % (34 of 36)	50.0 % (18 of 36)

1. 10E8p

KKKKDKWASL WNWFDITNWL WYIKLFIMIV GKKKKK

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	10E8p	natural abundance	protein	0.5 mM
8	HFIP	[U-2H]		25 % v/v
9	HEPES	natural abundance	buffer	2 mM
10	DSS	natural abundance		0.1 mM
11	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2NCT, Strand ID: A Detail

Release date

2016-04-18

Citation

Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface
Rujas, E., Partida-Hanon, A., Gulzar, N., Morante, K., Apellaniz, B., Garcia-Porras, M., Bruix, M., Tsumoto, K., Scott, J.K., Jimenez, M.K., Caaveiro, J.MM., Nieva, J.L.
Sci. Rep. (2016), 6, 38177-38177, PubMed 27905530 , DOI 10.1038/srep38177 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26034 released on 2016-04-18
Title NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of dodecylphosphocholine micelles

Related entities 1. membrane proximal external region of HIV-1 gp41 in hexafluoroisopropanol, : 1 : 1 : 1 : 26 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_26035_2nct.nef
Input source #2: Coordindates	2nct.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30------
KKKKDKWASLWNWFDITNWLWYIKLFIMIVGKKKKK
||||||||||||||||||||||||||||||||||||
KKKKDKWASLWNWFDITNWLWYIKLFIMIVGKKKKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0

Content subtype: combined_26035_2nct.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	347		100.0 (chain: A, length: 36)
2	Assigned chemical shifts	assigned_chem_shift_list_2	OK	174		83.3 (chain: A, length: 36)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	431 (1)	noe	97.2 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 247
  - ¹³C chemical shifts: 100
- Completeness of assignments
  - Entity_assemble_ID: A
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 83.3%
- Total number of assignments
  - ¹H chemical shifts: 174
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	281	247	87.9
¹³C chemical shifts	205	100	48.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	71	97.3
¹³C chemical shifts	72	36	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	176	84.6
¹³C chemical shifts	133	64	48.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	19	100.0
¹³C chemical shifts	19	19	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	44	100.0
¹³C chemical shifts	39	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	281	174	61.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	41	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	133	63.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	17	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	39	88.6

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 97.2%
- Total number of restraints: 431
- Weight of restraints: 1.0 (431)
- Potential type of restraints: upper-bound-parabolic (431)
- Range of distance target values: 2.31, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords HIV-1 gp41 protein, neutralizing epitope, peptide, peptide vaccine

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BMRB: 26035

Sample #1

Sample #2

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. membrane proximal external region of HIV-1 gp41 in hexafluoroisopropanol, : 1 : 1 : 1 : 26 entities Detail

Experiments performed 5 experiments Detail

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NMR combined restraints 4 contents Detail